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"examples/codon_models.rst", "examples/coevolution.rst", "examples/complete_seq_features.rst", "examples/empirical_protein_models.rst", "examples/hmm_par_heterogeneity.rst", "examples/index.rst", "examples/manipulating_tree_nodes.rst", "examples/neutral_test.rst", "examples/parallel.rst", "examples/parametric_bootstrap.rst", "examples/period_estimation.rst", "examples/phylo_by_ls.rst", "examples/rate_heterogeneity.rst", "examples/relative_rate.rst", "examples/scope_model_params_on_trees.rst", "examples/seq_features.rst", "examples/simple.rst", "examples/simulate_alignment.rst", "examples/testing_multi_loci.rst", "general.rst", "index.rst", "install.rst", "licenses.rst", "pycogent.rst"], "titles": ["available_apps", "available_codes", "available_models", "available_moltypes", "get_code", "get_model", "get_moltype", "load_aligned_seqs", "load_delimited", "load_seq", "load_table", "load_tree", "load_unaligned_seqs", "make_aligned_seqs", "make_seq", "make_table", "make_tree", 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"convert": [7, 9, 12, 13, 14, 17, 19, 20, 21, 24, 28, 30, 31, 32, 36, 64, 75, 76, 77, 81, 83, 111], "origin": [7, 9, 12, 13, 17, 19, 20, 21, 24, 38, 45, 66, 68, 75, 78, 81, 97, 101, 102, 103, 107, 124], "anoth": [7, 9, 12, 13, 17, 38, 45, 49, 53, 103, 107, 112], "dict": [7, 9, 10, 12, 13, 15, 17, 19, 20, 21, 25, 28, 30, 31, 32, 35, 36, 38, 50, 52, 97, 101, 109, 112], "option": [7, 9, 12, 19, 20, 44, 70, 72, 82, 103, 112, 116], "argument": [7, 9, 12, 13, 17, 19, 20, 21, 24, 28, 38, 43, 44, 53, 64, 66, 70, 72, 75, 76, 78, 80, 81, 83, 85, 88, 96, 101, 108, 109, 112], "parser": [7, 9, 10, 12, 34, 77], "type": [7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 20, 21, 23, 24, 28, 30, 31, 32, 35, 36, 38, 44, 47, 50, 62, 65, 66, 72, 76, 77, 81, 85, 88, 101, 103, 105, 116], "header": [8, 10, 15, 36, 48], "sep": [8, 10, 34, 36, 76, 81], "with_titl": [8, 36], "fals": [8, 10, 11, 16, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 34, 36, 38, 55, 57, 66, 72, 75, 81, 97, 105, 107, 109, 115], "with_legend": [8, 36], "limit": [8, 10, 15, 19, 20, 30, 31, 32, 34, 71, 72, 76, 81, 101, 114, 123], "kwarg": [8, 10, 15, 19, 20, 21, 28, 30, 31, 32, 36, 38], "basic": [8, 81, 97, 101, 107, 110, 112], "process": [8, 47, 49, 62, 72, 78, 106, 107, 109], "tabular": [8, 10, 34, 36, 74], "data": [8, 10, 13, 15, 17, 19, 20, 21, 23, 24, 28, 30, 31, 32, 36, 38, 44, 48, 51, 52, 53, 62, 63, 64, 65, 66, 72, 74, 75, 82, 87, 88, 97, 100, 109, 110, 112, 115, 116, 121, 123], "delimit": [8, 10, 34, 36, 75], "can": [8, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 35, 36, 38, 40, 41, 47, 48, 52, 53, 54, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 75, 76, 80, 82, 83, 84, 88, 90, 97, 99, 100, 101, 102, 103, 105, 107, 108, 109, 110, 111, 112, 115, 116, 117, 119, 122, 124], "begin": [8, 25, 97], "first": [8, 10, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 36, 38, 45, 48, 50, 52, 56, 64, 66, 68, 69, 72, 75, 76, 81, 97, 101, 102, 105, 107, 109, 111, 112, 115, 116], "line": [8, 10, 15, 19, 20, 21, 30, 31, 32, 38, 68, 101, 109], "after": [8, 10, 15, 19, 20, 28, 38, 65, 72, 75, 97, 101, 102, 103, 107, 109, 112], "titl": [8, 10, 15, 19, 20, 21, 36, 66, 86], "present": [8, 19, 20, 21, 28, 35, 38, 52, 58, 66, 68, 72, 75, 78, 101, 109, 124], "charact": [8, 10, 19, 20, 21, 23, 25, 28, 30, 31, 32, 36, 38, 46, 65, 68, 82, 90, 101, 102, 103], "separ": [8, 19, 20, 23, 30, 31, 32, 36, 38, 75, 76, 81, 101, 103, 107, 109, 112], "column": [8, 10, 15, 19, 20, 23, 34, 36, 38, 46, 49, 52, 78, 83, 102, 105], "last": [8, 19, 20, 23, 24, 28, 30, 31, 32, 38, 45, 53, 112], "legend": [8, 10, 15, 36, 86, 89], "int": [8, 19, 20, 21, 23, 25, 30, 31, 32, 36, 38, 109], "maximum": [8, 10, 15, 19, 20, 21, 30, 31, 32, 46, 49, 51, 52, 56, 62, 70, 89, 101, 108, 111, 114], "read": [8, 10, 11, 16, 25, 38, 76, 81, 97], "row": [8, 10, 15, 19, 20, 21, 23, 35, 36, 38, 48], "all": [8, 10, 11, 15, 16, 19, 20, 21, 23, 25, 27, 28, 30, 31, 32, 35, 36, 38, 41, 47, 50, 52, 53, 62, 64, 65, 70, 72, 75, 76, 77, 78, 81, 84, 86, 88, 101, 102, 103, 105, 108, 109, 110, 111, 112, 114, 115, 116, 117, 119, 122, 123, 124], "valu": [8, 10, 11, 15, 19, 20, 21, 23, 24, 30, 31, 32, 35, 36, 38, 40, 43, 48, 49, 50, 51, 52, 54, 56, 64, 66, 69, 71, 76, 82, 86, 93, 95, 96, 101, 102, 105, 107, 108, 109, 110, 111, 112, 114, 115, 116], "remain": [8, 19, 20, 38, 47, 49, 112, 115], "callabl": [9, 19, 20, 21, 24], "unalign": [9, 12, 17, 19, 21, 40, 41, 42, 64, 69, 86, 97], "which": [9, 12, 13, 15, 17, 19, 20, 21, 23, 24, 30, 31, 32, 36, 38, 45, 47, 50, 58, 62, 65, 66, 68, 70, 72, 75, 76, 80, 81, 82, 85, 88, 97, 101, 102, 103, 105, 107, 108, 109, 111, 112, 115, 116, 119, 123], "make": [9, 12, 13, 17, 19, 20, 21, 28, 30, 31, 32, 38, 44, 45, 64, 68, 77, 82, 101, 104, 106, 108, 111, 112, 113, 114, 115, 117, 119, 124], "object": [9, 12, 13, 14, 17, 19, 20, 21, 23, 28, 30, 31, 32, 35, 36, 38, 45, 48, 51, 52, 65, 72, 77, 78, 83, 85, 88, 97, 98, 99, 100, 102, 103, 104, 106, 108, 110, 112, 114], "keyword": [9, 12, 13, 17, 28, 43, 44, 64, 109], "pass": [9, 12, 13, 17, 19, 20, 21, 23, 24, 28, 30, 31, 32, 36, 38, 43, 44, 66, 70, 72, 75, 101, 109, 111, 112], "sequencecollect": [9, 12, 17, 20, 64, 75, 86, 87], "one": [9, 19, 20, 21, 23, 25, 28, 30, 31, 32, 36, 38, 47, 52, 53, 63, 66, 72, 77, 78, 80, 82, 87, 101, 102, 103, 105, 107, 108, 109, 112, 117], "us": [9, 10, 15, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 35, 36, 38, 44, 47, 48, 50, 51, 52, 59, 62, 64, 65, 68, 73, 74, 77, 83, 85, 87, 88, 90, 91, 95, 96, 97, 98, 99, 102, 103, 106, 107, 108, 110, 111, 113, 114, 115, 116, 117, 118, 119, 120, 123, 124], "load_aligned_seq": [9, 27, 66, 75], "load_unaligned_seq": [9, 27, 40, 41, 75], "get": [9, 20, 23, 25, 28, 30, 32, 35, 38, 45, 47, 50, 52, 62, 75, 77, 82, 97, 101, 103, 108, 109, 110, 114, 116, 119, 124], "collect": [9, 13, 17, 19, 21, 35, 38, 77, 86, 112], "reader": 10, "digit": [10, 15, 36], "4": [10, 15, 20, 21, 25, 36, 72, 83, 101, 109, 113, 118], "space": [10, 11, 15, 16, 19, 20, 30, 31, 32, 36, 70, 72, 93, 104, 107], "missing_data": [10, 15, 36], "max_width": [10, 15, 36], "1e": [10, 15, 36, 66], "100": [10, 15, 19, 20, 21, 36, 38, 66, 70, 96, 109], "index_nam": [10, 15, 35, 36, 76, 81], "column_templ": [10, 15, 36], "static_column_typ": [10, 76, 81], "simpl": [10, 15, 36, 45, 66, 72, 75, 82, 113, 118], "skip_inconsist": 10, "contain": [10, 11, 19, 20, 21, 23, 25, 28, 30, 31, 32, 36, 38, 45, 46, 47, 50, 63, 65, 66, 68, 72, 73, 81, 83, 103, 104, 107, 108, 110, 111], "between": [10, 15, 19, 20, 21, 24, 25, 28, 30, 31, 32, 36, 38, 40, 50, 53, 62, 72, 78, 81, 86, 87, 93, 101, 102, 105, 106, 108, 109, 112, 113, 116, 119], "thi": [10, 13, 15, 17, 19, 20, 21, 23, 24, 28, 30, 31, 32, 35, 36, 38, 40, 41, 45, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 70, 72, 75, 76, 78, 81, 82, 83, 85, 86, 88, 89, 90, 92, 97, 98, 99, 100, 101, 102, 103, 104, 105, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 118, 120, 122, 123, 124], "approach": [10, 30, 31, 32, 38, 45, 65, 66, 68, 71, 72, 86, 97, 101, 109, 111], "assum": [10, 19, 20, 30, 31, 32, 36, 66, 111], "numer": [10, 19, 20, 36, 54, 71, 101, 105, 116], "non": [10, 15, 19, 20, 21, 23, 28, 30, 31, 32, 36, 38, 46, 50, 62, 63, 68, 70, 76, 95, 101, 103, 121], "subsequ": [10, 78, 101, 115], "entri": [10, 20, 30, 31, 32, 50, 78, 86], "ar": [10, 11, 19, 20, 21, 23, 24, 25, 27, 28, 30, 31, 32, 36, 38, 44, 47, 48, 50, 51, 52, 56, 58, 62, 65, 66, 69, 70, 72, 75, 76, 78, 82, 83, 86, 88, 95, 96, 97, 100, 101, 102, 103, 107, 108, 109, 110, 111, 112, 114, 115, 116, 117, 121, 123, 124], "same": [10, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 36, 38, 40, 45, 66, 68, 81, 82, 96, 101, 103, 104, 105, 108, 109, 110, 111, 112, 115, 116, 119], "float": [10, 15, 19, 20, 23, 38, 103, 110], "point": [10, 15, 19, 20, 28, 30, 31, 32, 82, 88, 110, 115], "resolut": [10, 15, 19, 20, 21], "impli": [10, 15, 45, 123], "assign": [10, 19, 20, 28, 30, 31, 32, 38, 52, 53, 81, 101, 109, 115, 116], "ha": [10, 19, 20, 21, 23, 28, 30, 31, 32, 35, 38, 40, 42, 44, 49, 50, 52, 55, 62, 64, 65, 66, 72, 80, 83, 85, 88, 101, 103, 107, 108, 109, 115, 116, 124], "width": [10, 15, 19, 20, 21, 30, 31, 32, 36, 66, 86], "print": [10, 15, 19, 20, 21, 30, 31, 32, 65, 72, 101, 107, 108, 109, 112, 114, 115, 119], "kei": [10, 15, 19, 20, 21, 28, 30, 31, 32, 35, 36, 38, 48, 49, 50, 52, 62, 65, 66, 75, 76, 81, 109], "slice": [10, 15, 19, 20, 21, 97, 103, 111], "must": [10, 15, 19, 20, 21, 23, 24, 28, 30, 31, 32, 36, 38, 40, 41, 45, 66, 81, 82, 102, 103, 109, 115, 123], "uniqu": [10, 15, 19, 20, 36, 38, 52, 62, 76, 115, 121], "head": [10, 15, 36], "handl": [10, 15, 23, 28, 36, 38, 68, 78, 81, 82, 84, 102, 106], "exit": [10, 15, 47, 72], "mani": [10, 15, 28, 30, 31, 32, 45, 72, 77, 109, 110, 111, 121], "onli": [10, 11, 15, 19, 20, 21, 23, 28, 30, 31, 32, 36, 38, 49, 50, 52, 56, 65, 66, 72, 75, 80, 96, 100, 101, 103, 107, 110, 112, 113, 115, 117, 124], "appli": [10, 15, 19, 20, 21, 36, 62, 66, 68, 72, 75, 76, 81, 82, 90, 103, 105, 109, 110, 111, 115, 116], "pickl": [10, 15, 36, 76, 81, 100, 112], "output": [10, 15, 19, 20, 21, 36, 38, 44, 45, 47, 51, 52, 62, 66, 101, 103, 109], "when": [10, 15, 19, 20, 21, 36, 38, 47, 52, 63, 75, 88, 100, 103, 105, 107, 112, 122], "skip": [10, 19, 21, 76, 81], "have": [10, 15, 19, 20, 21, 25, 28, 30, 31, 32, 36, 38, 40, 41, 45, 52, 56, 58, 62, 64, 65, 66, 67, 72, 75, 78, 81, 82, 85, 86, 87, 88, 96, 97, 101, 103, 105, 107, 109, 111, 112, 113, 115, 116, 124], "differ": [10, 19, 20, 21, 23, 24, 25, 30, 31, 32, 36, 38, 47, 49, 50, 52, 53, 56, 62, 68, 72, 75, 78, 80, 88, 90, 97, 101, 103, 105, 106, 109, 111, 112, 114, 118, 119, 124], "length": [10, 19, 20, 21, 23, 28, 30, 31, 32, 38, 40, 41, 42, 50, 52, 54, 66, 68, 95, 101, 103, 108, 110, 111, 112, 114, 115, 118, 119], "underscore_unmung": [11, 16], "constructor": [11, 19, 20, 21, 28, 38], "tree": [11, 16, 19, 20, 21, 27, 38, 48, 52, 53, 62, 69, 84, 95, 96, 101, 104, 105, 106, 108, 114, 115, 117, 118, 119], "newick": [11, 16, 38, 48, 59], "xml": [11, 16, 38], "either": [11, 16, 19, 20, 21, 24, 35, 36, 45, 52, 62, 66, 78, 97, 103, 116], "json": [11, 19, 20, 21, 23, 28, 30, 31, 32, 38, 64, 72, 84, 95, 96, 100], "overrid": [11, 19, 20, 36, 38, 76, 78, 81], "replac": [11, 15, 16, 19, 20, 30, 31, 32, 36, 103, 124], "underscor": [11, 16], "e": [11, 16, 19, 20, 21, 23, 24, 28, 30, 31, 32, 35, 36, 38, 45, 46, 47, 64, 68, 72, 76, 81, 97, 101, 102, 103, 105, 107, 109, 116, 122], "sp_name": [11, 16], "becom": [11, 16, 28, 36, 64, 81, 107], "sp": [11, 16], "unmung": [11, 16], "turn": [11, 16, 30, 31, 32, 62, 86, 124], "off": [11, 16, 19, 20, 21, 65, 86], "although": [11, 16, 23, 76, 81, 97], "part": [11, 16, 23, 38, 64, 72, 75, 105, 109, 115], "cogent3": [11, 19, 20, 21, 23, 24, 25, 30, 31, 32, 38, 40, 41, 45, 47, 51, 62, 65, 66, 71, 72, 75, 76, 78, 81, 83, 86, 87, 97, 101, 102, 105, 108, 110, 112, 114, 121, 122], "support": [11, 19, 20, 38, 47, 64, 70, 75, 76, 81, 82, 84, 88, 109, 112], "phylonod": [11, 16, 80, 107], "sourc": [13, 17, 75, 120, 123], "initi": [13, 17, 38, 72, 82, 101, 105, 107, 115], "unknown": [13, 17], "ad": [13, 17, 19, 20, 21, 36, 38, 62, 70, 97, 107, 112, 116], "class": [13, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 34, 35, 36, 38, 45, 47, 56, 62, 64, 65, 66, 70, 72, 75, 78, 81, 86, 101, 107, 110, 111, 112], "seq": [14, 19, 20, 21, 23, 25, 28, 30, 31, 32, 97, 111], "raw": [14, 23, 36, 47, 97], "row_ord": 15, "data_fram": 15, "2d": [15, 30, 31, 32], "tupl": [15, 19, 20, 21, 23, 28, 30, 31, 32, 35, 38, 66, 101, 112], "If": [15, 19, 20, 21, 23, 24, 28, 30, 31, 32, 35, 36, 38, 40, 41, 45, 47, 48, 50, 59, 66, 68, 72, 75, 76, 78, 81, 82, 86, 87, 97, 101, 103, 105, 109, 112, 115, 120], "top": [15, 27, 36, 43, 44, 45, 70, 78, 95], "level": [15, 27, 43, 44, 45, 78, 81, 82, 96, 109], "common": [15, 23, 38, 53, 102, 115], "label": [15, 19, 20, 21, 28, 30, 31, 32, 36, 38, 93, 105, 116], "each": [15, 19, 20, 21, 23, 28, 30, 31, 32, 36, 38, 47, 48, 50, 66, 70, 72, 81, 88, 103, 105, 107, 108, 109, 112, 119], "order": [15, 19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 35, 36, 38, 45, 66, 68, 70, 72, 84, 97, 104, 107, 112, 115], "pull": [15, 19, 20], "twoddict": 15, "miss": [15, 28, 30, 31, 32, 66, 68], "panda": [15, 36], "datafram": [15, 36], "supersed": 15, "treestr": 16, "tip_nam": [16, 38, 115], "initialis": 16, "tip": [16, 38, 53, 70, 107, 115], "star": 16, "topologi": [16, 38, 70, 72], "indic": [16, 19, 20, 21, 23, 28, 30, 31, 32, 36, 38, 45, 52, 55, 56, 64, 65, 66, 88, 89, 96, 101, 109], "arg": [19, 20, 23, 30, 31, 32, 38], "add_annot": [19, 30, 31, 32, 116], "klass": [19, 24, 30, 31, 32], "add_featur": [19, 30, 31, 32, 116], "span": [19, 25, 30, 31, 32, 66, 103, 116], "add_from_ref_aln": [19, 20, 66], "ref_aln": [19, 20, 66], "before_nam": [19, 20, 21, 66], "after_nam": [19, 20, 21, 66], "insert": [19, 20, 21, 38, 107], "": [19, 20, 21, 23, 25, 30, 31, 32, 35, 36, 38, 47, 55, 57, 59, 62, 64, 68, 72, 76, 78, 81, 90, 92, 97, 100, 101, 103, 104, 105, 107, 108, 111, 112, 114, 115, 117, 119, 120, 122], "self": [19, 20, 21, 23, 24, 25, 28, 30, 31, 32, 36, 38], "base": [19, 20, 21, 23, 25, 28, 30, 31, 32, 35, 38, 47, 62, 81, 82, 97, 102, 109], "refer": [19, 20, 21, 64, 68, 72, 75, 80, 81, 84, 105], "0": [19, 20, 21, 23, 24, 25, 30, 31, 32, 36, 38, 51, 66, 72, 80, 81, 96, 97, 101, 103, 105, 107, 108, 109, 111, 112, 113, 115], "By": [19, 20, 21, 45, 60, 61, 68, 75, 88, 101, 108], "append": [19, 20, 21, 36, 38, 47, 107], "end": [19, 20, 21, 30, 31, 32, 36, 38, 47, 66, 93, 103, 105, 109, 112], "chang": [19, 20, 21, 23, 24, 25, 28, 38, 45, 52, 58, 66, 78, 80, 86, 95, 101, 105, 112, 124], "seri": [19, 20, 23, 35, 36, 70, 77, 103, 109], "add": [19, 20, 23, 24, 30, 31, 32, 35, 66, 68, 75, 80, 85, 103, 107, 112], "new": [19, 20, 21, 23, 24, 28, 30, 31, 32, 35, 36, 38, 80, 101, 107, 108, 113, 124], "structur": [19, 20, 38, 124], "ref_nam": [19, 20, 21], "befor": [19, 20, 21, 28, 38, 86, 101, 102, 119], "both": [19, 20, 21, 30, 31, 32, 36, 38, 62, 64, 66, 70, 75, 112, 115], "exampl": [19, 20, 23, 24, 27, 30, 31, 32, 40, 41, 50, 53, 55, 57, 58, 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parameters": [[50, "global-parameters"]], "Motif parameters": [[50, "motif-parameters"]], "Testing a hypothesis \u2013 non-stationary or time-reversible": [[51, "testing-a-hypothesis-non-stationary-or-time-reversible"]], "hypothesis_result has attributes and keys": [[51, "hypothesis-result-has-attributes-and-keys"]], "Accessing the test statistics": [[51, "accessing-the-test-statistics"]], "The null hypothesis": [[51, "the-null-hypothesis"]], "The alternate hypothesis": [[51, "the-alternate-hypothesis"]], "Saving hypothesis results": [[51, "saving-hypothesis-results"]], "Apply a non-stationary nucleotide model to an alignment with 3 sequences": [[52, "apply-a-non-stationary-nucleotide-model-to-an-alignment-with-3-sequences"]], "model_result": [[52, "model-result"]], "Fitting a separate nucleotide model to each codon position": [[52, "fitting-a-separate-nucleotide-model-to-each-codon-position"]], "Specifying a non-stationary model with time-heterogeneous parameters": [[53, "specifying-a-non-stationary-model-with-time-heterogeneous-parameters"]], "Specify a distinct rate matrix for the great apes": [[53, "specify-a-distinct-rate-matrix-for-the-great-apes"]], "Apply a non-stationary nucleotide model to an alignment with a tree": [[54, "apply-a-non-stationary-nucleotide-model-to-an-alignment-with-a-tree"]], "Specify the tree via a tree instance": [[54, "specify-the-tree-via-a-tree-instance"]], "Specify the tree via a path.": [[54, "specify-the-tree-via-a-path"]], "Apply the model to an alignment": [[54, "apply-the-model-to-an-alignment"]], "natsel_neutral \u2013 a test for selective neutrality": [[55, "natsel-neutral-a-test-for-selective-neutrality"]], "natsel_sitehet \u2013 a test of site heterogeneity": [[56, "natsel-sitehet-a-test-of-site-heterogeneity"]], "Getting the individual site posterior probabilities": [[56, "getting-the-individual-site-posterior-probabilities"]], "natsel_timehet \u2013 a test of branch heterogeneity": [[57, "natsel-timehet-a-test-of-branch-heterogeneity"]], "natsel_zhang \u2013 a branch-site test": [[58, "natsel-zhang-a-branch-site-test"]], "Getting the posterior probabilities of site-class membership": [[58, "getting-the-posterior-probabilities-of-site-class-membership"]], "Getting all the statistics in tabular form": [[58, "getting-all-the-statistics-in-tabular-form"]], "Applying GNC, a non-stationary codon model": [[59, "applying-gnc-a-non-stationary-codon-model"]], "We can obtain the tree with branch lengths as ENS": [[59, "we-can-obtain-the-tree-with-branch-lengths-as-ens"]], "Applying a time-reversible codon model": [[60, "applying-a-time-reversible-codon-model"]], "Using the conditional nucleotide form codon model": [[60, "using-the-conditional-nucleotide-form-codon-model"]], "Applying a time-reversible nucleotide model": [[61, "applying-a-time-reversible-nucleotide-model"]], "Using the GTR model": [[61, "using-the-gtr-model"]], "The apps": [[62, "the-apps"]], "Overview": [[62, "overview"]], "The progressive_align App": [[62, "the-progressive-align-app"]], "The model App": [[62, "the-model-app"]], "The hypothesis App": [[62, "the-hypothesis-app"]], "The natsel Apps": [[62, "the-natsel-apps"]], "Write your own Apps": [[62, "write-your-own-apps"]], "Tracking records that could not be processed": [[63, "tracking-records-that-could-not-be-processed"]], "The NotCompleted object": [[63, "the-notcompleted-object"]], "NotCompleted FALSE type": [[63, "notcompleted-false-type"]], "NotCompleted ERROR type": [[63, "notcompleted-error-type"]], "Composed functions propagate NotCompleted results": [[63, "composed-functions-propagate-notcompleted-results"]], "Turn your functions into composable apps": [[64, "turn-your-functions-into-composable-apps"]], "A simple example": [[64, "a-simple-example"]], "Renaming sequences": [[64, "renaming-sequences"]], "A user app with a different output type": [[64, "a-user-app-with-a-different-output-type"]], "Sequence": [[65, "sequence"]], "DNA and RNA sequences": [[65, "dna-and-rna-sequences"]], "Creating a DNA sequence from a string": [[65, "creating-a-dna-sequence-from-a-string"]], "Creating a RNA sequence from a string": [[65, "creating-a-rna-sequence-from-a-string"]], "Converting to FASTA format": [[65, "converting-to-fasta-format"]], "Convert a RNA sequence to FASTA format": [[65, "convert-a-rna-sequence-to-fasta-format"]], "Creating a named sequence": [[65, "creating-a-named-sequence"]], "Setting or changing the name of a sequence": [[65, "setting-or-changing-the-name-of-a-sequence"]], "Complementing a DNA sequence": [[65, "complementing-a-dna-sequence"]], "Reverse complementing a DNA sequence": [[65, "reverse-complementing-a-dna-sequence"]], "Translate a DnaSequence to protein": [[65, "translate-a-dnasequence-to-protein"]], "Converting a DNA sequence to RNA": [[65, "converting-a-dna-sequence-to-rna"]], "Convert an RNA sequence to DNA": [[65, "convert-an-rna-sequence-to-dna"]], "Testing complementarity": [[65, "testing-complementarity"]], "Joining two DNA sequences": [[65, "joining-two-dna-sequences"]], "Slicing DNA sequences": [[65, "slicing-dna-sequences"]], "Getting 3rd positions from codons": [[65, "getting-3rd-positions-from-codons"]], "Getting 1st and 2nd positions from codons": [[65, "getting-1st-and-2nd-positions-from-codons"]], "Return a randomized version of the sequence": [[65, "return-a-randomized-version-of-the-sequence"]], "Remove gaps from a sequence": [[65, "remove-gaps-from-a-sequence"]], "Sequence Collections and Alignments": [[66, "sequence-collections-and-alignments"]], "What\u2019s the difference between Alignment and ArrayAlignment?": [[66, "what-s-the-difference-between-alignment-and-arrayalignment"]], "Basic Collection objects": [[66, "basic-collection-objects"]], "Constructing a SequenceCollection or Alignment object from strings": [[66, "constructing-a-sequencecollection-or-alignment-object-from-strings"]], "Constructing a ArrayAlignment using make_aligned_seqs": [[66, "constructing-a-arrayalignment-using-make-aligned-seqs"]], "Converting a SequenceCollection to FASTA format": [[66, "converting-a-sequencecollection-to-fasta-format"]], "Adding new sequences to an existing collection or alignment": [[66, "adding-new-sequences-to-an-existing-collection-or-alignment"]], "Appending the sequences": [[66, "appending-the-sequences"]], "Inserting the sequences": [[66, "inserting-the-sequences"]], "Inserting sequence(s) based on their alignment to a reference sequence": [[66, "inserting-sequence-s-based-on-their-alignment-to-a-reference-sequence"]], "Removing all columns with gaps in a named sequence": [[66, "removing-all-columns-with-gaps-in-a-named-sequence"]], "The elements of a collection or alignment": [[66, "the-elements-of-a-collection-or-alignment"]], "Accessing individual sequences from a collection or alignment by name": [[66, "accessing-individual-sequences-from-a-collection-or-alignment-by-name"]], "Slice the sequences from an alignment like a list": [[66, "slice-the-sequences-from-an-alignment-like-a-list"]], "Getting a subset of sequences from the alignment": [[66, "getting-a-subset-of-sequences-from-the-alignment"]], "Alignments": [[66, "alignments"]], "Creating an Alignment object from a SequenceCollection": [[66, "creating-an-alignment-object-from-a-sequencecollection"]], "Convert alignment to DNA, RNA or PROTEIN moltypes": [[66, "convert-alignment-to-dna-rna-or-protein-moltypes"]], "Handling gaps": [[66, "handling-gaps"]], "Remove all gaps from an alignment in FASTA format": [[66, "remove-all-gaps-from-an-alignment-in-fasta-format"]], "Writing sequences to file": [[66, "writing-sequences-to-file"]], "Converting an alignment to FASTA format": [[66, "converting-an-alignment-to-fasta-format"]], "Converting an alignment into Phylip format": [[66, "converting-an-alignment-into-phylip-format"]], "Converting an alignment to a list of strings": [[66, "converting-an-alignment-to-a-list-of-strings"]], "Slicing an alignment": [[66, "slicing-an-alignment"]], "By rows (sequences)": [[66, "by-rows-sequences"]], "Getting a single column from an alignment": [[66, "getting-a-single-column-from-an-alignment"]], "Getting a region of contiguous columns": [[66, "getting-a-region-of-contiguous-columns"]], "Iterating over alignment positions": [[66, "iterating-over-alignment-positions"]], "Getting codon 3rd positions from Alignment": [[66, "getting-codon-3rd-positions-from-alignment"]], "Getting codon 3rd positions from ArrayAlignment": [[66, "getting-codon-3rd-positions-from-arrayalignment"]], "Filtering positions": [[66, "filtering-positions"]], "Trim terminal stop codons": [[66, "trim-terminal-stop-codons"]], "Eliminating columns with non-nucleotide characters": [[66, "eliminating-columns-with-non-nucleotide-characters"]], "Getting all variable positions from an alignment": [[66, "getting-all-variable-positions-from-an-alignment"]], "Getting all constant positions from an alignment": [[66, "getting-all-constant-positions-from-an-alignment"]], "Getting all variable codons from an alignment": [[66, "getting-all-variable-codons-from-an-alignment"]], "Filtering sequences": [[66, "filtering-sequences"]], "Extracting sequences by sequence identifier into a new alignment object": [[66, "extracting-sequences-by-sequence-identifier-into-a-new-alignment-object"]], "Extracting sequences using an arbitrary function into a new alignment object": [[66, "extracting-sequences-using-an-arbitrary-function-into-a-new-alignment-object"]], "Computing alignment statistics": [[66, "computing-alignment-statistics"]], "Getting motif counts": [[66, "getting-motif-counts"]], "Computing motif probabilities from an alignment": [[66, "computing-motif-probabilities-from-an-alignment"]], "Working with alignment gaps": [[66, "working-with-alignment-gaps"]], "Filtering extracted columns for the gap character": [[66, "filtering-extracted-columns-for-the-gap-character"]], "Calculating the gap fraction": [[66, "calculating-the-gap-fraction"]], "Extracting maps of aligned to unaligned positions (i.e., gap maps)": [[66, "extracting-maps-of-aligned-to-unaligned-positions-i-e-gap-maps"]], "Filtering alignments based on gaps": [[66, "filtering-alignments-based-on-gaps"]], "Alphabets": [[67, "alphabets"]], "Alphabet and MolType": [[67, "alphabet-and-moltype"]], "Creating tuple alphabets": [[67, "creating-tuple-alphabets"]], "Convert a sequence into integers": [[67, "convert-a-sequence-into-integers"]], "Convert integers to a sequence": [[67, "convert-integers-to-a-sequence"]], "Annotations": [[68, "annotations"]], "Annotations with coordinates": [[68, "annotations-with-coordinates"]], "Automated introduction from reading genbank files": [[68, "automated-introduction-from-reading-genbank-files"]], "Customising annotation construction from reading a genbank file": [[68, "customising-annotation-construction-from-reading-a-genbank-file"]], "Creating directly on a sequence": [[68, "creating-directly-on-a-sequence"]], "Via": [[68, "via"]], "add_annotation": [[68, "add-annotation"]], "add_feature": [[68, "add-feature"]], "Adding as a series or item-wise": [[68, "adding-as-a-series-or-item-wise"]], "Taking the union of annotations": [[68, "taking-the-union-of-annotations"]], "Getting annotation coordinates": [[68, "getting-annotation-coordinates"]], "Annotations have shadows": [[68, "annotations-have-shadows"]], "Adding to a sequence member of an alignment": [[68, "adding-to-a-sequence-member-of-an-alignment"]], "Adding to an alignment": [[68, "adding-to-an-alignment"]], "Slicing sequences and alignments by annotations": [[68, "slicing-sequences-and-alignments-by-annotations"]], "Slicing by pseudo-feature or feature series": [[68, "slicing-by-pseudo-feature-or-feature-series"]], "Slice series must not be overlapping": [[68, "slice-series-must-not-be-overlapping"]], "You can slice an annotation itself": [[68, "you-can-slice-an-annotation-itself"]], "Sequence vs Alignment slicing": [[68, "sequence-vs-alignment-slicing"]], "Copying annotations": [[68, "copying-annotations"]], "Querying": [[68, "querying"]], "Querying produces objects only valid for their source": [[68, "querying-produces-objects-only-valid-for-their-source"]], "Querying for absent annotation": [[68, "querying-for-absent-annotation"]], "Querying features that span gaps in alignments": [[68, "querying-features-that-span-gaps-in-alignments"]], "as_one_span unifies features with discontinuous alignment coordinates": [[68, "as-one-span-unifies-features-with-discontinuous-alignment-coordinates"]], "Behaviour of annotations on nucleic acid sequences": [[68, "behaviour-of-annotations-on-nucleic-acid-sequences"]], "Masking annotated regions": [[68, "masking-annotated-regions"]], "Masking annotated regions on alignments": [[68, "masking-annotated-regions-on-alignments"]], "You can take mask of the shadow": [[68, "you-can-take-mask-of-the-shadow"]], "What features of a certain type are available?": [[68, "what-features-of-a-certain-type-are-available"]], "Getting all features of a type, or everything but that type": [[68, "getting-all-features-of-a-type-or-everything-but-that-type"]], "Getting sequence features when you have an alignment object": [[68, "getting-sequence-features-when-you-have-an-alignment-object"]], "Annotation display on sequences": [[68, "annotation-display-on-sequences"]], "Todo": [[68, "id1"], [68, "id2"], [75, "id1"], [85, "id1"], [86, "id1"], [100, "id1"], [105, "id1"]], "Building alignments": [[69, "building-alignments"]], "Using a cogent3 progressive aligner for nucleotides": [[69, "using-a-cogent3-progressive-aligner-for-nucleotides"]], "Using a cogent3 progressive aligner for codons": [[69, "using-a-cogent3-progressive-aligner-for-codons"]], "Converting gaps from aa-seq alignment to nuc seq alignment": [[69, "converting-gaps-from-aa-seq-alignment-to-nuc-seq-alignment"]], "Building phylogenies": [[70, "building-phylogenies"]], "Building A Phylogenetic Tree From Pairwise Distances": [[70, "building-a-phylogenetic-tree-from-pairwise-distances"]], "Directly via alignment.quick_tree()": [[70, "directly-via-alignment-quick-tree"]], "Using the DistanceMatrix object": [[70, "using-the-distancematrix-object"]], "Explicitly via DistanceMatrix and cogent3.phylo.nj.nj()`": [[70, "explicitly-via-distancematrix-and-cogent3-phylo-nj-nj"]], "Directly from a pairwise distance dict": [[70, "directly-from-a-pairwise-distance-dict"]], "By Least-squares": [[70, "by-least-squares"]], "By ML": [[70, "by-ml"]], "Genetic distance calculation": [[71, "genetic-distance-calculation"]], "Fast pairwise distance estimation": [[71, "fast-pairwise-distance-estimation"]], "Computing genetic distances using the Alignment object": [[71, "computing-genetic-distances-using-the-alignment-object"]], "Using the distance calculator directly": [[71, "using-the-distance-calculator-directly"]], "Likelihood based pairwise distance estimation": [[71, "likelihood-based-pairwise-distance-estimation"]], "Evolutionary Analysis Using Likelihood": [[72, "evolutionary-analysis-using-likelihood"]], "Specifying substitution models": [[72, "specifying-substitution-models"]], "The available pre-defined substitution models": [[72, "the-available-pre-defined-substitution-models"]], "Getting a substitution model with get_model()": [[72, "getting-a-substitution-model-with-get-model"]], "Rate heterogeneity models": [[72, "rate-heterogeneity-models"]], "For nucleotide": [[72, "for-nucleotide"]], "For codon": [[72, "for-codon"]], "For protein": [[72, "for-protein"]], "Making a likelihood function": [[72, "making-a-likelihood-function"]], "Providing an alignment to a likelihood function": [[72, "providing-an-alignment-to-a-likelihood-function"]], "Scoping parameters on trees \u2013 time heterogeneous models": [[72, "scoping-parameters-on-trees-time-heterogeneous-models"]], "Specifying a parameter as constant": [[72, "specifying-a-parameter-as-constant"]], "Providing a starting value for a parameter": [[72, "providing-a-starting-value-for-a-parameter"]], "Setting parameter bounds for optimisation": [[72, "setting-parameter-bounds-for-optimisation"]], "Setting an upper bound for branch length": [[72, "setting-an-upper-bound-for-branch-length"]], "Specifying rate heterogeneity functions": [[72, "specifying-rate-heterogeneity-functions"]], "Specifying Phylo-HMMs": [[72, "specifying-phylo-hmms"]], "Fitting likelihood functions - Choice of optimisers": [[72, "fitting-likelihood-functions-choice-of-optimisers"]], "How to check your optimisation was successful": [[72, "how-to-check-your-optimisation-was-successful"]], "Overview of the fitted likelihood function": [[72, "overview-of-the-fitted-likelihood-function"]], "Log likelihood and number of free parameters": [[72, "log-likelihood-and-number-of-free-parameters"]], "Aikake Information Criterion": [[72, "aikake-information-criterion"]], "Bayesian Information Criterion": [[72, "bayesian-information-criterion"]], "Getting maximum likelihood estimates": [[72, "getting-maximum-likelihood-estimates"]], "One at a time": [[72, "one-at-a-time"]], "Just the motif probabilities": [[72, "just-the-motif-probabilities"]], "As tables": [[72, "as-tables"]], "Testing Hypotheses - Using Likelihood Ratio Tests": [[72, "testing-hypotheses-using-likelihood-ratio-tests"]], "Testing Hypotheses - By parametric bootstrapping": [[72, "testing-hypotheses-by-parametric-bootstrapping"]], "Determining confidence intervals on MLEs": [[72, "determining-confidence-intervals-on-mles"]], "Saving results": [[72, "saving-results"]], "Reconstructing ancestral sequences": [[72, "reconstructing-ancestral-sequences"]], "Translate DNA sequences": [[73, "translate-dna-sequences"]], "Translate all six frames": [[73, "translate-all-six-frames"]], "Find out how many stops in a frame": [[73, "find-out-how-many-stops-in-a-frame"]], "Translate a codon": [[73, "translate-a-codon"]], "Look up the amino acid corresponding to a single codon": [[73, "look-up-the-amino-acid-corresponding-to-a-single-codon"]], "Get all the codons for one amino acid": [[73, "get-all-the-codons-for-one-amino-acid"]], "Get all the codons for a group of amino acids": [[73, "get-all-the-codons-for-a-group-of-amino-acids"]], "Converting the CodonAlphabet to codon series": [[73, "converting-the-codonalphabet-to-codon-series"]], "Obtaining the codons from a DnaSequence object": [[73, "obtaining-the-codons-from-a-dnasequence-object"]], "Translating a DNA sequence with a terminating stop codon": [[73, "translating-a-dna-sequence-with-a-terminating-stop-codon"]], "By removing the trailing stop codon first": [[73, "by-removing-the-trailing-stop-codon-first"]], "By slicing the DnaSequence first": [[73, "by-slicing-the-dnasequence-first"]], "Cookbook": [[74, "cookbook"]], "Loading an alignment from a file or url": [[75, "loading-an-alignment-from-a-file-or-url"]], "Loading aligned sequences": [[75, "loading-aligned-sequences"]], "Loading unaligned sequences": [[75, "loading-unaligned-sequences"]], "Loading from a url": [[75, "loading-from-a-url"], [76, "loading-from-a-url"], [81, "loading-from-a-url"]], "Specifying the file format": [[75, "specifying-the-file-format"]], "Specifying the sequence molecular type": [[75, "specifying-the-sequence-molecular-type"]], "Making an alignment from standard python objects": [[75, "making-an-alignment-from-standard-python-objects"]], "From a dict of strings": [[75, "from-a-dict-of-strings"]], "From a series of strings": [[75, "from-a-series-of-strings"]], "Stripping label characters on loading": [[75, "stripping-label-characters-on-loading"]], "Making a sequence collection from standard python objects": [[75, "making-a-sequence-collection-from-standard-python-objects"]], "Loading sequences using format parsers": [[75, "loading-sequences-using-format-parsers"]], "Loading FASTA sequences from an open file or list of lines": [[75, "loading-fasta-sequences-from-an-open-file-or-list-of-lines"]], "Handling overloaded FASTA sequence labels": [[75, "handling-overloaded-fasta-sequence-labels"]], "Loading a csv file": [[76, "loading-a-csv-file"], [81, "loading-a-csv-file"]], "Loading delimited specifying the format": [[76, "loading-delimited-specifying-the-format"], [81, "loading-delimited-specifying-the-format"]], "Loading delimited data without a header line": [[76, "loading-delimited-data-without-a-header-line"], [81, "loading-delimited-data-without-a-header-line"]], "Using load_delimited()": [[76, "using-load-delimited"], [81, "using-load-delimited"]], "Using FilteringParser": [[76, "using-filteringparser"], [81, "using-filteringparser"]], "Selectively loading parts of a big file": [[76, "selectively-loading-parts-of-a-big-file"], [81, "selectively-loading-parts-of-a-big-file"]], "Loading a set number of lines from a file": [[76, "loading-a-set-number-of-lines-from-a-file"], [81, "loading-a-set-number-of-lines-from-a-file"]], "Loading only some rows": [[76, "loading-only-some-rows"], [81, "loading-only-some-rows"]], "Loading only some columns": [[76, "loading-only-some-columns"], [81, "loading-only-some-columns"]], "Load raw data as a list of lists of strings": [[76, "load-raw-data-as-a-list-of-lists-of-strings"], [81, "load-raw-data-as-a-list-of-lists-of-strings"]], "Make a table from header and rows": [[76, "make-a-table-from-header-and-rows"], [81, "make-a-table-from-header-and-rows"]], "Make a table from a dict": [[76, "make-a-table-from-a-dict"], [81, "make-a-table-from-a-dict"]], "Specify the column order when creating from a dict.": [[76, "specify-the-column-order-when-creating-from-a-dict"], [81, "specify-the-column-order-when-creating-from-a-dict"]], "Create the table with an index": [[76, "create-the-table-with-an-index"], [81, "create-the-table-with-an-index"]], "Create a table from a pandas.DataFrame": [[76, "create-a-table-from-a-pandas-dataframe"], [81, "create-a-table-from-a-pandas-dataframe"]], "Create a table from header and rows": [[76, "create-a-table-from-header-and-rows"], [81, "create-a-table-from-header-and-rows"]], "Create a table from dict": [[76, "create-a-table-from-dict"], [81, "create-a-table-from-dict"]], "Create a table from a 2D dict": [[76, "create-a-table-from-a-2d-dict"], [81, "create-a-table-from-a-2d-dict"]], "Create a table that has complex python objects as elements": [[76, "create-a-table-that-has-complex-python-objects-as-elements"], [81, "create-a-table-that-has-complex-python-objects-as-elements"]], "Create an empty table": [[76, "create-an-empty-table"], [81, "create-an-empty-table"]], "Manipulating biological data": [[77, "manipulating-biological-data"]], "Sequences and Alignments": [[77, "sequences-and-alignments"]], "Genetic code": [[77, "genetic-code"]], "Trees": [[77, "trees"], [80, "trees"]], "Molecular types": [[78, "molecular-types"]], "Available molecular types": [[78, "available-molecular-types"]], "Getting a MolType": [[78, "getting-a-moltype"]], "Using a MolType to get ambiguity codes": [[78, "using-a-moltype-to-get-ambiguity-codes"]], "MolType definition of degenerate codes": [[78, "moltype-definition-of-degenerate-codes"]], "Nucleic acid MolType and complementing": [[78, "nucleic-acid-moltype-and-complementing"]], "Making sequences": [[78, "making-sequences"]], "Verify sequences": [[78, "verify-sequences"]], "Making a custom MolType": [[78, "making-a-custom-moltype"]], "Protein sequences": [[79, "protein-sequences"]], "Creating a ProteinSequence with a name": [[79, "creating-a-proteinsequence-with-a-name"]], "Converting a DNA sequence string to protein sequence string": [[79, "converting-a-dna-sequence-string-to-protein-sequence-string"]], "Loading protein sequences from a Phylip file": [[79, "loading-protein-sequences-from-a-phylip-file"]], "Loading a tree from a file and visualizing it with ascii_art()": [[80, "loading-a-tree-from-a-file-and-visualizing-it-with-ascii-art"]], "Writing a tree to a file": [[80, "writing-a-tree-to-a-file"]], "Getting the individual nodes of a tree by name": [[80, "getting-the-individual-nodes-of-a-tree-by-name"]], "Getting the name of a node (or a tree)": [[80, "getting-the-name-of-a-node-or-a-tree"]], "The object type of a tree and its nodes is the same": [[80, "the-object-type-of-a-tree-and-its-nodes-is-the-same"]], "Working with the nodes of a tree": [[80, "working-with-the-nodes-of-a-tree"]], "Getting the path between two tips or edges (connecting edges)": [[80, "getting-the-path-between-two-tips-or-edges-connecting-edges"]], "Getting the distance between two nodes": [[80, "getting-the-distance-between-two-nodes"]], "Getting the last common ancestor (LCA) for two nodes": [[80, "getting-the-last-common-ancestor-lca-for-two-nodes"]], "Getting all the ancestors for a node": [[80, "getting-all-the-ancestors-for-a-node"]], "Getting all the children for a node": [[80, "getting-all-the-children-for-a-node"]], "Getting all the distances for a tree": [[80, "getting-all-the-distances-for-a-tree"]], "Getting the two nodes that are farthest apart": [[80, "getting-the-two-nodes-that-are-farthest-apart"]], "Get the nodes within a given distance": [[80, "get-the-nodes-within-a-given-distance"]], "Rerooting trees": [[80, "rerooting-trees"]], "At a named node": [[80, "at-a-named-node"]], "At the midpoint": [[80, "at-the-midpoint"]], "Near a given tip": [[80, "near-a-given-tip"]], "Tree representations": [[80, "tree-representations"]], "Newick format": [[80, "newick-format"]], "XML format": [[80, "xml-format"]], "Tree traversal": [[80, "tree-traversal"]], "Preorder": [[80, "preorder"]], "Postorder": [[80, "postorder"]], "Selecting subtrees": [[80, "selecting-subtrees"]], "One way to do it": [[80, "one-way-to-do-it"]], "Tree manipulation methods": [[80, "tree-manipulation-methods"]], "Pruning the tree": [[80, "pruning-the-tree"]], "Create a full unrooted copy of the tree": [[80, "create-a-full-unrooted-copy-of-the-tree"]], "Transform tree into a bifurcating tree": [[80, "transform-tree-into-a-bifurcating-tree"]], "Transform tree into a balanced tree": [[80, "transform-tree-into-a-balanced-tree"]], "Test two trees for same topology": [[80, "test-two-trees-for-same-topology"]], "Calculate each node\u2019s maximum distance to a tip": [[80, "calculate-each-node-s-maximum-distance-to-a-tip"]], "Scale branch lengths in place to integers for ascii output": [[80, "scale-branch-lengths-in-place-to-integers-for-ascii-output"]], "Get tip-to-tip distances": [[80, "get-tip-to-tip-distances"]], "Compare two trees using tip-to-tip distance matrices": [[80, "compare-two-trees-using-tip-to-tip-distance-matrices"]], "Tabular data": [[81, "tabular-data"]], "Adding a new column": [[81, "adding-a-new-column"], [81, "id1"]], "Add a title and a legend to a table": [[81, "add-a-title-and-a-legend-to-a-table"]], "Iterating over table rows": [[81, "iterating-over-table-rows"]], "How many rows are there?": [[81, "how-many-rows-are-there"]], "How many columns are there?": [[81, "how-many-columns-are-there"]], "Iterating over table columns": [[81, "iterating-over-table-columns"]], "Table slicing using column names": [[81, "table-slicing-using-column-names"]], "Table slicing using indices": [[81, "table-slicing-using-indices"]], "Changing displayed numerical precision": [[81, "changing-displayed-numerical-precision"]], "Change digits or column spacing": [[81, "change-digits-or-column-spacing"]], "Wrapping tables for display": [[81, "wrapping-tables-for-display"]], "Display the top of a table using head()": [[81, "display-the-top-of-a-table-using-head"]], "Display the bottom of a table using tail()": [[81, "display-the-bottom-of-a-table-using-tail"]], "Display random rows from a table": [[81, "display-random-rows-from-a-table"]], "Change the number of rows displayed by repr()": [[81, "change-the-number-of-rows-displayed-by-repr"]], "Changing column headings": [[81, "changing-column-headings"]], "Create a new column from existing ones": [[81, "create-a-new-column-from-existing-ones"]], "Get table data as a numpy array": [[81, "get-table-data-as-a-numpy-array"]], "Get a table column as a list": [[81, "get-a-table-column-as-a-list"]], "Get multiple table columns as a list": [[81, "get-multiple-table-columns-as-a-list"]], "Get the table as a row oriented dict": [[81, "get-the-table-as-a-row-oriented-dict"]], "Get the table as a column oriented dict": [[81, "get-the-table-as-a-column-oriented-dict"]], "Get the table as a pandas.DataFrame": [[81, "get-the-table-as-a-pandas-dataframe"]], "Get a table of counts as a contingency table": [[81, "get-a-table-of-counts-as-a-contingency-table"]], "Appending tables": [[81, "appending-tables"]], "Summing a single column": [[81, "summing-a-single-column"]], "Summing multiple columns or rows - strictly numerical data": [[81, "summing-multiple-columns-or-rows-strictly-numerical-data"]], "Summing multiple columns or rows with mixed non-numeric/numeric data": [[81, "summing-multiple-columns-or-rows-with-mixed-non-numeric-numeric-data"]], "Filtering table rows": [[81, "filtering-table-rows"]], "Filtering table columns": [[81, "filtering-table-columns"]], "Standard sorting": [[81, "standard-sorting"]], "Reverse sorting": [[81, "reverse-sorting"]], "Sorting involving multiple columns, one reversed": [[81, "sorting-involving-multiple-columns-one-reversed"]], "Getting raw data for a single column": [[81, "getting-raw-data-for-a-single-column"]], "Getting raw data for multiple columns": [[81, "getting-raw-data-for-multiple-columns"]], "Getting distinct values": [[81, "getting-distinct-values"]], "Counting occurrences of values": [[81, "counting-occurrences-of-values"]], "Counting unique values": [[81, "counting-unique-values"]], "Joining or merging tables": [[81, "joining-or-merging-tables"]], "Transpose a table": [[81, "transpose-a-table"]], "Specify markdown as the str() format": [[81, "specify-markdown-as-the-str-format"]], "Specify latex as the str() format": [[81, "specify-latex-as-the-str-format"]], "Get a table as a markdown formatted string": [[81, "get-a-table-as-a-markdown-formatted-string"]], "Get a table as a latex formatted string": [[81, "get-a-table-as-a-latex-formatted-string"]], "Get a table as a restructured text csv-table": [[81, "get-a-table-as-a-restructured-text-csv-table"]], "Get a table as a restructured text grid table": [[81, "get-a-table-as-a-restructured-text-grid-table"]], "Getting a latex format table with to_string()": [[81, "getting-a-latex-format-table-with-to-string"]], "Getting a bedGraph format with to_string()": [[81, "getting-a-bedgraph-format-with-to-string"]], "Getting a table as html": [[81, "getting-a-table-as-html"]], "What formats can be written?": [[81, "what-formats-can-be-written"]], "Writing a latex formmated file": [[81, "writing-a-latex-formmated-file"]], "Writing delimited formats": [[81, "writing-delimited-formats"]], "Useful Utilities": [[82, "useful-utilities"]], "UnionDict \u2013 a dict with set like operations and keys as attributes": [[82, "uniondict-a-dict-with-set-like-operations-and-keys-as-attributes"]], "Accessing elements of a UnionDict": [[82, "accessing-elements-of-a-uniondict"]], "Updating a UnionDict": [[82, "updating-a-uniondict"]], "Accessing a non-existent UnionDict key": [[82, "accessing-a-non-existent-uniondict-key"]], "Using Cogent3\u2019s optimisers for your own functions": [[82, "using-cogent3-s-optimisers-for-your-own-functions"]], "Miscellaneous functions": [[82, "miscellaneous-functions"]], "Force a variable to be iterable": [[82, "force-a-variable-to-be-iterable"]], "Curry a function": [[82, "curry-a-function"]], "Test to see if an object is iterable": [[82, "test-to-see-if-an-object-is-iterable"]], "Test to see if an object is a single char": [[82, "test-to-see-if-an-object-is-a-single-char"]], "Flatten a deeply nested iterable": [[82, "flatten-a-deeply-nested-iterable"]], "Test to determine if list of tuple": [[82, "test-to-determine-if-list-of-tuple"]], "Create a case-insensitive iterable": [[82, "create-a-case-insensitive-iterable"]], "Construct a distance matrix lookup function": [[82, "construct-a-distance-matrix-lookup-function"]], "Check class types": [[82, "check-class-types"]], "Delegate to a separate object": [[82, "delegate-to-a-separate-object"]], "Wrap a function to hide from a class": [[82, "wrap-a-function-to-hide-from-a-class"]], "Construct a constrained container": [[82, "construct-a-constrained-container"]], "Available genetic codes": [[83, "available-genetic-codes"]], "Getting a genetic code with get_code()": [[83, "getting-a-genetic-code-with-get-code"]], "Data Files Used in the Documentation": [[84, "data-files-used-in-the-documentation"]], "Coevolution analysis": [[85, "coevolution-analysis"]], "Display coevolution as a heatmap": [[85, "display-coevolution-as-a-heatmap"]], "Display coevolution scores as a Violin plot": [[85, "display-coevolution-scores-as-a-violin-plot"]], "Display coevolution scores as a Boxplot": [[85, "display-coevolution-scores-as-a-boxplot"]], "Dotplot basics": [[86, "dotplot-basics"]], "Modifying the matching parameters": [[86, "modifying-the-matching-parameters"]], "Displaying dotplot for the reverse complement": [[86, "displaying-dotplot-for-the-reverse-complement"]], "Setting plot attributes": [[86, "setting-plot-attributes"]], "Dotplot with annotated sequences": [[87, "dotplot-with-annotated-sequences"]], "Reloading from json": [[87, "reloading-from-json"]], "Removing annotation tracks": [[87, "removing-annotation-tracks"]], "Counting gaps per sequence": [[88, "counting-gaps-per-sequence"]], "Plotting counts of unique gaps": [[88, "plotting-counts-of-unique-gaps"]], "Displaying unique gaps as a bar chart": [[88, "displaying-unique-gaps-as-a-bar-chart"]], "Displaying unique gaps as a violin plot": [[88, "displaying-unique-gaps-as-a-violin-plot"]], "Displaying unique gaps as a box plot": [[88, "displaying-unique-gaps-as-a-box-plot"]], "Information analysis of an alignment": [[89, "information-analysis-of-an-alignment"]], "Illustrated with a simple example": [[89, "illustrated-with-a-simple-example"]], "On a sample data set": [[89, "on-a-sample-data-set"]], "Sequence logos": [[90, "sequence-logos"]], "Drawing logo for a TFBS": [[90, "drawing-logo-for-a-tfbs"]], "Drawing a sequence logo from a multiple sequence alignment": [[90, "drawing-a-sequence-logo-from-a-multiple-sequence-alignment"]], "Sequence logo of protein alignment": [[90, "sequence-logo-of-protein-alignment"]], "Image Gallery": [[91, "image-gallery"]], "Alignments & Sequences": [[91, "alignments-sequences"]], "Phylogenetic Trees": [[91, "phylogenetic-trees"]], "Angular Dendrogram Style": [[92, "angular-dendrogram-style"]], "With Contemporaneous Tips": [[92, "with-contemporaneous-tips"], [93, "with-contemporaneous-tips"], [94, "with-contemporaneous-tips"], [95, "with-contemporaneous-tips"]], "Circular Dendrogram Style": [[93, "circular-dendrogram-style"]], "Colouring a set of edges": [[93, "colouring-a-set-of-edges"], [95, "colouring-a-set-of-edges"]], "Radial Dendrogram Style": [[94, "radial-dendrogram-style"]], "Square Dendrogram Style": [[95, "square-dendrogram-style"]], "Showing Bootstrap Support": [[96, "showing-bootstrap-support"]], "Change the placement of support text": [[96, "change-the-placement-of-support-text"]], "Map protein alignment gaps to DNA alignment gaps": [[97, "map-protein-alignment-gaps-to-dna-alignment-gaps"]], "Make a UPGMA cluster": [[98, "make-a-upgma-cluster"]], "Make a neighbor joining tree": [[99, "make-a-neighbor-joining-tree"]], "Calculate pairwise distances between sequences": [[100, "calculate-pairwise-distances-between-sequences"]], "Using codon models": [[101, "using-codon-models"]], "Constructing the codon substitution model": [[101, "constructing-the-codon-substitution-model"]], "Standard test of neutrality": [[101, "standard-test-of-neutrality"]], "Rate-heterogeneity model variants": [[101, "rate-heterogeneity-model-variants"]], "Mixing branch and site-heterogeneity": [[101, "mixing-branch-and-site-heterogeneity"]], "Perform a coevolutionary analysis on biological sequence alignments": [[102, "perform-a-coevolutionary-analysis-on-biological-sequence-alignments"]], "Annotating alignments and sequences": [[103, "annotating-alignments-and-sequences"]], "Use an empirical protein substitution model": [[104, "use-an-empirical-protein-substitution-model"]], "Evaluate process heterogeneity using a Hidden Markov Model": [[105, "evaluate-process-heterogeneity-using-a-hidden-markov-model"]], "Model Ho: no rate heterogeneity": [[105, "model-ho-no-rate-heterogeneity"]], "Model Ha(1): two classes of gamma distributed but independent sites": [[105, "model-ha-1-two-classes-of-gamma-distributed-but-independent-sites"]], "Model Ha(2): fast and slowly evolving sites are auto-correlated": [[105, "model-ha-2-fast-and-slowly-evolving-sites-are-auto-correlated"]], "A model with patches of kappa": [[105, "a-model-with-patches-of-kappa"]], "Tutorials": [[106, "tutorials"]], "Data manipulation": [[106, "data-manipulation"]], "General data analysis": [[106, "general-data-analysis"]], "Modelling Evolution": [[106, "modelling-evolution"]], "Phylogenetic Reconstruction": [[106, "phylogenetic-reconstruction"]], "Utilities": [[106, "utilities"]], "Manipulation of Tree Node Objects": [[107, "manipulation-of-tree-node-objects"]], "An Example of Conditional Tree Node Modifications": [[107, "an-example-of-conditional-tree-node-modifications"]], "A test of the neutral theory": [[108, "a-test-of-the-neutral-theory"]], "Parallel computations": [[109, "parallel-computations"]], "Parallel computation on a single computer": [[109, "parallel-computation-on-a-single-computer"]], "Using app.apply_to()": [[109, "using-app-apply-to"]], "Directly using cogent3.util.parallel.map()": [[109, "directly-using-cogent3-util-parallel-map"]], "Parallel computation on multiple computers": [[109, "parallel-computation-on-multiple-computers"]], "Performing a parametric bootstrap": [[110, "performing-a-parametric-bootstrap"]], "Estimating periodic signals": [[111, "estimating-periodic-signals"]], "Estimating the periods in a signal": [[111, "estimating-the-periods-in-a-signal"]], "For numerical (continuous) data": [[111, "for-numerical-continuous-data"], [111, "id1"]], "Discrete Fourier transform": [[111, "discrete-fourier-transform"]], "Auto-correlation": [[111, "auto-correlation"]], "For symbolic data": [[111, "for-symbolic-data"], [111, "id2"], [111, "id4"]], "Estimating power for specified period": [[111, "estimating-power-for-specified-period"]], "Measuring statistical significance of periodic signals": [[111, "measuring-statistical-significance-of-periodic-signals"]], "For numerical (continuous data)": [[111, "id3"]], "Permutation testing": [[111, "permutation-testing"]], "Phylogenetic reconstruction by least squares": [[112, "phylogenetic-reconstruction-by-least-squares"]], "Look for the single best tree": [[112, "look-for-the-single-best-tree"]], "A more rigorous tree space search": [[112, "a-more-rigorous-tree-space-search"]], "Assessing the fit for a pre-specified tree topology": [[112, "assessing-the-fit-for-a-pre-specified-tree-topology"]], "Using maximum likelihood for measuring tree fit": [[112, "using-maximum-likelihood-for-measuring-tree-fit"]], "Analysis of rate heterogeneity": [[113, "analysis-of-rate-heterogeneity"]], "Performing a relative rate test": [[114, "performing-a-relative-rate-test"]], "Allowing substitution model parameters to differ between branches": [[115, "allowing-substitution-model-parameters-to-differ-between-branches"]], "Specifying a clade": [[115, "specifying-a-clade"]], "Specifying a stem": [[115, "specifying-a-stem"]], "Specifying clade and stem": [[115, "specifying-clade-and-stem"]], "Alternate arguments for specifying edges": [[115, "alternate-arguments-for-specifying-edges"]], "Applications of scoped parameters": [[115, "applications-of-scoped-parameters"]], "Advanced sequence handling": [[116, "advanced-sequence-handling"]], "The simplest script": [[117, "the-simplest-script"]], "Simulate an alignment": [[118, "simulate-an-alignment"]], "Likelihood analysis of multiple loci": [[119, "likelihood-analysis-of-multiple-loci"]], "Posting Bugs": [[120, "posting-bugs"]], "Citation": [[120, "citation"]], "Support": [[120, "support"]], "Documentation": [[121, "documentation"]], "Installation": [[122, "installation"]], "Minimal installation": [[122, "minimal-installation"]], "Install with graphing tools": [[122, "install-with-graphing-tools"]], "Install with developer tools": [[122, "install-with-developer-tools"]], "Installing the development version": [[122, "installing-the-development-version"]], "Installing using conda": [[122, "installing-using-conda"]], "Manual creation of the conda environment": [[122, "manual-creation-of-the-conda-environment"]], "License": [[123, "license"]], "Cogent3 License": [[123, "cogent3-license"]], "How does cogent3 relate to PyCogent?": [[124, "how-does-cogent3-relate-to-pycogent"]], "cogent3 no longer includes module x, what do I do?": [[124, "cogent3-no-longer-includes-module-x-what-do-i-do"]]}, "indexentries": {"available_apps() (in module cogent3.__init__)": [[0, "cogent3.__init__.available_apps"]], "available_codes() (in module cogent3.__init__)": [[1, "cogent3.__init__.available_codes"]], "available_models() (in module cogent3.__init__)": [[2, "cogent3.__init__.available_models"]], "available_moltypes() (in module cogent3.__init__)": [[3, "cogent3.__init__.available_moltypes"]], "get_code() (in module cogent3.__init__)": [[4, "cogent3.__init__.get_code"]], "get_model() (in 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"attach_annotations() (alignment method)": [[19, "cogent3.core.alignment.Alignment.attach_annotations"]], "clear_annotations() (alignment method)": [[19, "cogent3.core.alignment.Alignment.clear_annotations"]], "coevolution() (alignment method)": [[19, "cogent3.core.alignment.Alignment.coevolution"]], "copy() (alignment method)": [[19, "cogent3.core.alignment.Alignment.copy"]], "copy_annotations() (alignment method)": [[19, "cogent3.core.alignment.Alignment.copy_annotations"]], "count_gaps_per_pos() (alignment method)": [[19, "cogent3.core.alignment.Alignment.count_gaps_per_pos"]], "count_gaps_per_seq() (alignment method)": [[19, "cogent3.core.alignment.Alignment.count_gaps_per_seq"]], "counts() (alignment method)": [[19, "cogent3.core.alignment.Alignment.counts"]], "counts_per_pos() (alignment method)": [[19, "cogent3.core.alignment.Alignment.counts_per_pos"]], "counts_per_seq() (alignment method)": [[19, "cogent3.core.alignment.Alignment.counts_per_seq"]], "deepcopy() (alignment 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